I’m still quite new to WaniKani and have been going through Level 1. I am having trouble understanding why there is both a Kanji meaning and a vocabulary meaning. Also, sometimes the Kanji and vocabulary meanings will be different, sometimes the same.
How do I know whether the Kanji and vocab meanings are different or the same?
Can anyone explain this in simple terms without any complex jargon? Thanks.
The kanji are the 2000+ individual characters this site will be teaching you – kanji can have multiple readings, referred to as on’yomi (Chinese-derived) readings and kun’yomi (Japanese) readings
Sometimes only one reading will be taught for both the kanji and vocab item, and sometimes you’ll learn one reading for the kanji and a different one for the vocab, it really just depends 
Kanji are the individual characters, and the vocab are actual words
The background color during lessons/reviews will let you know whether the item you’re looking at is a radical, kanji, or vocab:
It might seem pretty complicated at first, but as you keep progressing, you’ll get a better feel for how the system works and it’ll become a lot more second nature to you to know which meanings/readings WK is asking for ^^
がんばってね ! 
EDIT: It’s better to get familiar with what on’yomi and kun’yomi readings are now to set a good foundation of understanding moving forward, so here’s an article by Tofugu (the creators of this site) that goes into more detail about what they are 
Japanese kanji, like Chinese characters, have inherent meanings. The meaning inherent in the character can sometimes be subtly different to the meaning of a vocabulary word which uses this character.
Kanji are building blocks for words, but sometimes a single building block is enough to form a word. Kanji are more flexible than vocabulary, they can be read in multiple ways, and can mean different things. For vocab this is generally more restricted. You will have to learn it first without thinking too hard, there is not really a clear system 
For example in level 2 you have 本, which has meanings book, origin, real, main in WK. When you see 本 alone it could be a book and read as ほん, or a base/origin/cause with reading もと, in compounds it could be 一本 (いっぽん) for counting pencils or something, in 本店 (ほんてん) it is the main store, not a book store …
The kanji means many things, but depending on how you read it it turns into a vocabulary word with a clear(er) meaning.
Everything the others on this thread have said is absolutely right. I’ll only add another way to say it.
While vocabulary on this site are actual words used in Japanese, kanji should be thought of as potential words. The meaning given in WaniKani to kanji is really only a hint to what they might mean in a word.
You can think of Chinese as something like the Latin and Greek of Japanese, and kanji as something like the Latin and Greek roots that form many English words. Think of a word like "Mediterranean”. “Medi” isn’t really a word in English but you might recognize it from “medium” as having a meaning like “middle”. Similarly with “Terra”, you may know that it means “Earth”. So put them together and you have “middle earth”, which is in fact the original meaning of “Mediterranean”. But we know that Mediterranean now refers to a sea or region that we no longer think of as the middle of the Earth. Kanji work the same way in Japanese as do Latin and Greek roots of English words: they have their inherent meanings and can be combined to form words whose meanings may diverge from their roots.
And because kanji don’t have fixed phonetics, they can also be used for Japanese words that didn’t derive from Chinese, and in these cases, they use native Japanese rather than (historical) Chinese readings or pronunciations.
Thank you for the article, it is very useful!
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